As well, please post in this thread any ideas you have. So far weve established that legendaries are essentially just dangerously strong pokemon, they do not make the world turn. Also, tasteful editing will be required on many pokemon if youre following their pokedex entries. Pokemon cannot be hotter than the sun and what not. IF legendaries are found or roused, wherever and however that may be, the general consensus is that the regime are the only ones with the resources to kill/capture them. Of course, being the regime they are, if captured they will be misused for the regime's personal gain. I.e. Zapdos captured, imprisoned in a huge complex and guarded prison, and its electricity harness for personal use by the regime. One idea is that the regime have developed a pokeball/control device of some kind allowing them to harness pokemon against their will. That is how they came to be so powerful, they have sheer numbers and power. Also, we'll need to discuss and agree upon a guideline for pokemon intelligence and its role. Are all pokemon on level with humans as far as intelligence yet restricted physically, or will intelligence depend on species. I.e. Magikarp would not be very bright. If we gave them even a basic intelligence and knowledge of what is "right or wrong", one could safely assume pokemon and humans could enter into a partnership or trainer dominant relationship without pokeballs. They would submit to the relationship, thus forming the of trainer and partner. This would really solidify a bond between pokemon and trainer if they werent just captured, they have a role in ending up with you. It also opens up doors for rebels without access to pokeballs. It would add another aspect to their stories. Youre not just in hiding and on the run alone, its WITH your pokemon, outside of its pokeball and everything. 

Ive posted a CS (character sheet) to reference to.